Filtered variants in 24 SRNS associated genes
| Gene | Variant | Patients Affected (Heterozygote Unless Hom-Homozygous) | dbSNP Ref. No. (Build 135) | MAF If Available or ESP Genotype Count | HGMDa (Authors’ Comments) | PolyPhen | MutPred |
|---|---|---|---|---|---|---|---|
| ACTN4 | Arg310Gln | 23 | rs112545413 | A=0.0055 | FSGS (but also in controls) | Benign | 0.459 |
| APOL1 | Val369Glu | 20 | rs143845266 | ESP: AT-0.003 TT-0.997 | No | Probably damaging | 0.831 |
| APOL1 | Gly247Arg | 15 | rs146925617 | ESP: AG-0.001 GG-0.999 | No | Benign | 0.516 |
| APOL1 | Asn403fs | 1, 30 | rs143830837 | No data | No | n/a | n/a |
| CD2AP | Pro566Ser | 2 | Not in dbSNP | ESP: TC-0.0002 CC-0.9998 | No | Benign | 0.389 |
| COL4A4 | Ala715Val | 7 | rs76636743 | A=0.0014 | No | Benign | 0.282 |
| COL4A4 | Ala1558Val | 7 | Not in dbSNP | No data | No | Unknown | 0.418 |
| COL4A4 | Arg877Gln | 6 | rs150979437 | ESP: TC-0.005 CC-0.995 | No | Unknown | 0.526 |
| COL4A4 | Ser969b | 24 (hom) | rs35138315 | No data | Alport syndrome | n/a | n/a |
| COL4A4 | Gly999Glu | 23, 29 | rs13027659 | T=0.0073 | No | Unknown | 0.6 |
| COL4A4 | Met1399Leu | 17 | rs149117087 | No data | No | Unknown | 0.508 |
| COQ2 | Asn228Ser | 8 | rs121918232 | No data | Coenzyme Q10 deficiency | Probably damaging | 0.75 |
| COQ2 | Leu234fs | 8 | Not in dbSNP | No data | No | n/a | n/a |
| INF2 | Arg877Gln | 7 | rs142678449 | ESP: AA-0.0004 AG-0.0168 GG-0.9828 | No | Unknown | 0.447 |
| INF2 | Glu593Lys | 28 | Not in dbSNP | No data | No | Unknown | 0.502 |
| INF2 | Ile685Va | 19, 29 | Not in dbSNP | ESP: GA-0.0002 AA-0.9998 | No | Unknown | 0.527 |
| INF2 | Val557Gly | 19 | Not in dbSNP | ESP: GT-0.004 TT-0.996 | No | Unknown | 0.512 |
| LAMB2 | Gly1676Ile | 33 | Not in dbSNP | No data | No | Benign | 0.233 |
| LAMB2 | Arg575Gln | 28 | rs61729152 | T=0.0087 | No | Benign | 0.566 |
| MYH9 | Lys910Gln | 23 (hom) | Not in dbSNP | No data | Fechtner syndrome (but also in control) | Possibly damaging | 0.368 |
| MYH9 | Ala1072Thr | 2 | Not in dbSNP | No data | No | Benign | 0.357 |
| MYH9 | Lys1775Glu | 14 | rs145139708 | C=0.002 | No | Benign | 0.561 |
| MYH9 | Arg1936Gln | 10 | Not in dbSNP | No data | No | Possibly damaging | 0.203 |
| MYO1E | Ile531Met | 34 | rs140447165 | C =0.002 | No | Possibly damaging | 0.634 |
| NPHS1 | His1174Tyr | 21 | rs115489112 | A=0.0018 | No | Possibly damaging | 0.431 |
| NPHS1 | Asn1077Ser | 1, 4, 5, 7, 8, 9, 15, 26, 30 (21 hom) | rs4806213 | C=0.0836 | CNS (but also in control) | Possibly damaging | 0.269 |
| NPHS1 | Arg408Gln | 16, 26 | rs33950747 | T=0.0297 | CNS (but also in control) | Possibly damaging | 0.892 |
| NPHS1 | Pro264Arg | 22, 32, 35, 36 | rs34982899 | C=0.0105 | CNS (in a single patient as a compound het) | Benign | 0.77 |
| NPHS1 | Ala806Gly | 2 (hom) | Not in dbSNP | No data | No | Possibly damaging | 0.805 |
| NPHS1 | Glu117Lys | 11, 16, 18, 24, 25, 26, 35, 36 (1, 2, 4, 12, 20, 30 hom) | rs3814995 | T=0.3423 | CNS (but also in control) | Possibly damaging | 0.802 |
| NPHS1 | Arg586Gly | 1, 4, 30 (hom) | Not in dbSNP | No data | FSGS | Benign | 0.824 |
| NPHS1 | Ala916Ser | 6 | rs138173172 | ESP: AC 0.006 CC 0.994 | Reported in 1 patient with minimal change | Possibly damaging | 0.72 |
| NPHS1 | Thr294Ile | 9, 10 | rs113825926 | A=0.0037 | Reported in 1 patient with minimal change | Benign | 0.296 |
| NPHS1 | Val1084fs | 3 (hom) | Not in dbSNP | No data | CNS | n/a | n/a |
| NPHS2 | Pro20Leu | 17 | rs74315344 | A=0.0014 | Nephrotic syndrome, steroid-resistant | n/a | 0.721 |
| NPHS2 | Arg229Gln | 6, 10, 27 | rs61747728 | T=0.0178 | FSGS | Possibly damaging | 0.698 |
| NPHS2 | Ala284Val | 23 (hom) | Not in dbSNP | No data | Nephrotic syndrome, steroid-resistant | Possibly damaging | 0.945 |
| NPHS2 | Phe344fs | 6, 10 | Not in dbSNP | No data | FSGS | n/a | n/a |
| PLCE1 | Arg321b | 5 (hom) | Not in dbSNP | No data | FSGS | n/a | n/a |
| PLCE1 | Leu57Phe | 19, 29 | Not in dbSNP | No data | No | Possibly damaging | 0.106 |
| PMM2 | Glu197Ala | 13 | rs34258285 | C=0.0119 | Congenital disorder of glycosylation 1a (but polymorphism) | Benign | 0.826 |
| PTPRO | His362Arg | 34 | rs141042273 | ESP: AA-0.999 AG-0.001 | No | Benign | 0.392 |
| SMARCAL1 | Glu377Gln | 12 | rs2066518 | C=0.0603 | Schimke immuno-osseous dysplasia (report not clearly pathogenic) | Possibly damaging | 0.492 |
| WT1 | Ala100Gly | 1, 4 (hom) | Not in dbSNP | No data | No | Benign | 0.723 |
Variants of note in the exome of 24 genes associated with steroid-resistant nephrotic syndrome (SRNS) sequenced in 36 patients. Includes all variants described in Human Genome Mutation Database (HGMD) professional, all novel variants (not being described in single-nucleotide polymorphisms database [dbSNP] or the 1000 Genomes Project), and all variants with an minor allele frequency (MAF)<1% in the 1000 Genomes Project (http://www.1000genomes.org/node/506; allele frequency) or if not available, Exome Variant Server, National Heart, Lung and Blood Institute Exome Sequencing Project (ESP), Seattle, WA (http://evs.gs.washington.edu/EVS/). Where possible, MutPred and PolyPhen scores are also provided. CNS, congenital nephrotic syndrome; n/a, not available.
↵a Professional release: December of 2011.
↵b Nonsense.